This repository contains the Fireprot pipeline written in Common Workflow Language.

This pipeline relies on the Subworkflow feature of CWL which enables us to include multiple CWL files into one main CWL file as subworkflows. Thanks to this feature we can divide pipelines into logical modules for simpler maintenance.

The main pipeline file is called fireprot.cwl, it transitively includes all other CWL files in this repository. CWL files in the root of this repository are either simple command line tools (e.g. btc.cwl) or they are workflows that utilize the Subworkflow feature and include CWL files from a direcotry of the same name (e.g. multimutants.cwl includes all CWL files from multimutants).

This repository also contains a script that starts the pipeline on CWL-WES server running in CERIT-SC Kubernetes infrastructure.